From a51c8bef714d8d5718952d1190e2781118a6c0d2 Mon Sep 17 00:00:00 2001 From: CI Date: Thu, 12 Sep 2024 16:01:34 +0000 Subject: [PATCH] Build branch v0.1 with version v0.1.0 (3143dd6) Build pipeline: viash-hub.craftbox.v0.1-6rdzs Source commit: https://github.com/viash-hub/craftbox/commit/3143dd6e4c2c3107f79639fe8602d92f3141ad82 Source message: (Re-) release v0.1.0l --- CHANGELOG.md | 2 +- _viash.yaml | 3 +- nextflow.config | 2 +- .../executable/concat_text/.config.vsh.yaml | 14 +++--- target/executable/concat_text/concat_text | 20 ++++---- target/executable/csv2fasta/.config.vsh.yaml | 14 +++--- target/executable/csv2fasta/csv2fasta | 20 ++++---- target/executable/untar/.config.vsh.yaml | 14 +++--- target/executable/untar/untar | 20 ++++---- target/nextflow/concat_text/.config.vsh.yaml | 14 +++--- target/nextflow/concat_text/main.nf | 47 ++++++++++++------- target/nextflow/concat_text/nextflow.config | 2 +- target/nextflow/csv2fasta/.config.vsh.yaml | 14 +++--- target/nextflow/csv2fasta/main.nf | 47 ++++++++++++------- target/nextflow/csv2fasta/nextflow.config | 2 +- target/nextflow/untar/.config.vsh.yaml | 14 +++--- target/nextflow/untar/main.nf | 47 ++++++++++++------- target/nextflow/untar/nextflow.config | 2 +- 18 files changed, 166 insertions(+), 132 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e271d2..5ad7192 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# craftbox x.x.x +# craftbox 0.1.0 ## NEW FEATURES diff --git a/_viash.yaml b/_viash.yaml index 4b02f50..b29ae47 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,5 @@ name: craftbox +version: v0.1.0 description: | A collection of custom-tailored scripts and applied tools. license: MIT @@ -7,7 +8,7 @@ links: issue_tracker: https://github.com/viash-hub/craftbox/issues repository: https://github.com/viash-hub/craftbox -viash_version: 0.9.0-RC7 +viash_version: 0.9.0 config_mods: | .requirements.commands := ['ps'] diff --git a/nextflow.config b/nextflow.config index 99294bb..4b337e8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ manifest { name = "craftbox" - version = "v0.1" + version = "v0.1.0" defaultBranch = "main" nextflowVersion = "!>=20.12.1-edge" } diff --git a/target/executable/concat_text/.config.vsh.yaml b/target/executable/concat_text/.config.vsh.yaml index 302ae72..168e2aa 100644 --- a/target/executable/concat_text/.config.vsh.yaml +++ b/target/executable/concat_text/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "concat_text" -version: "v0.1" +version: "v0.1.0" authors: - name: "Toni Verbeiren" roles: @@ -152,7 +152,7 @@ engines: id: "docker" image: "alpine:latest" target_registry: "images.viash-hub.com" - target_tag: "v0.1" + target_tag: "v0.1.0" namespace_separator: "/" setup: - type: "apk" @@ -170,22 +170,22 @@ build_info: engine: "docker|native" output: "target/executable/concat_text" executable: "target/executable/concat_text/concat_text" - viash_version: "0.9.0-RC7" - git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295" + viash_version: "0.9.0" + git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82" git_remote: "https://github.com/viash-hub/craftbox" package_config: name: "craftbox" - version: "v0.1" + version: "v0.1.0" description: "A collection of custom-tailored scripts and applied tools.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" keywords: - "scripts" - "custom" diff --git a/target/executable/concat_text/concat_text b/target/executable/concat_text/concat_text index 80608f6..8e67bc1 100755 --- a/target/executable/concat_text/concat_text +++ b/target/executable/concat_text/concat_text @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# concat_text v0.1 +# concat_text v0.1.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "concat_text v0.1" + echo "concat_text v0.1.0" echo "" echo "Concatenate a number of text files, handle gzipped text files gracefully and" echo "optionally gzip the output text file." @@ -479,10 +479,10 @@ RUN apk add --no-cache bash procps file LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component concat_text" -LABEL org.opencontainers.image.created="2024-09-12T15:43:28Z" +LABEL org.opencontainers.image.created="2024-09-12T15:57:23Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox" -LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295" -LABEL org.opencontainers.image.version="v0.1" +LABEL org.opencontainers.image.revision="3143dd6e4c2c3107f79639fe8602d92f3141ad82" +LABEL org.opencontainers.image.version="v0.1.0" VIASHDOCKER fi @@ -618,7 +618,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "concat_text v0.1" + echo "concat_text v0.1.0" exit ;; --input) @@ -742,7 +742,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/concat_text:v0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/concat_text:v0.1.0' fi # print dockerfile diff --git a/target/executable/csv2fasta/.config.vsh.yaml b/target/executable/csv2fasta/.config.vsh.yaml index e917abc..d5935f0 100644 --- a/target/executable/csv2fasta/.config.vsh.yaml +++ b/target/executable/csv2fasta/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "csv2fasta" -version: "v0.1" +version: "v0.1.0" argument_groups: - name: "Inputs" arguments: @@ -192,7 +192,7 @@ engines: id: "docker" image: "python:slim" target_registry: "images.viash-hub.com" - target_tag: "v0.1" + target_tag: "v0.1.0" namespace_separator: "/" setup: - type: "apt" @@ -221,22 +221,22 @@ build_info: engine: "docker|native" output: "target/executable/csv2fasta" executable: "target/executable/csv2fasta/csv2fasta" - viash_version: "0.9.0-RC7" - git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295" + viash_version: "0.9.0" + git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82" git_remote: "https://github.com/viash-hub/craftbox" package_config: name: "craftbox" - version: "v0.1" + version: "v0.1.0" description: "A collection of custom-tailored scripts and applied tools.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" keywords: - "scripts" - "custom" diff --git a/target/executable/csv2fasta/csv2fasta b/target/executable/csv2fasta/csv2fasta index eb680c4..4bcd168 100755 --- a/target/executable/csv2fasta/csv2fasta +++ b/target/executable/csv2fasta/csv2fasta @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# csv2fasta v0.1 +# csv2fasta v0.1.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "csv2fasta v0.1" + echo "csv2fasta v0.1.0" echo "" echo "Convert two columns from a CSV file to FASTA entries. The CSV file can" echo "contain an optional header and each row (other than the header) becomes" @@ -525,10 +525,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "dnaio" LABEL org.opencontainers.image.description="Companion container for running component csv2fasta" -LABEL org.opencontainers.image.created="2024-09-12T15:43:27Z" +LABEL org.opencontainers.image.created="2024-09-12T15:57:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox" -LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295" -LABEL org.opencontainers.image.version="v0.1" +LABEL org.opencontainers.image.revision="3143dd6e4c2c3107f79639fe8602d92f3141ad82" +LABEL org.opencontainers.image.version="v0.1.0" VIASHDOCKER fi @@ -664,7 +664,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "csv2fasta v0.1" + echo "csv2fasta v0.1.0" exit ;; --input) @@ -848,7 +848,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/csv2fasta:v0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/csv2fasta:v0.1.0' fi # print dockerfile diff --git a/target/executable/untar/.config.vsh.yaml b/target/executable/untar/.config.vsh.yaml index c343749..529e515 100644 --- a/target/executable/untar/.config.vsh.yaml +++ b/target/executable/untar/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "untar" -version: "v0.1" +version: "v0.1.0" argument_groups: - name: "Input arguments" arguments: @@ -129,7 +129,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.1" + target_tag: "v0.1.0" namespace_separator: "/" setup: - type: "apt" @@ -146,22 +146,22 @@ build_info: engine: "docker|native" output: "target/executable/untar" executable: "target/executable/untar/untar" - viash_version: "0.9.0-RC7" - git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295" + viash_version: "0.9.0" + git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82" git_remote: "https://github.com/viash-hub/craftbox" package_config: name: "craftbox" - version: "v0.1" + version: "v0.1.0" description: "A collection of custom-tailored scripts and applied tools.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" keywords: - "scripts" - "custom" diff --git a/target/executable/untar/untar b/target/executable/untar/untar index ed86cbd..c1daf33 100755 --- a/target/executable/untar/untar +++ b/target/executable/untar/untar @@ -1,10 +1,10 @@ #!/usr/bin/env bash -# untar v0.1 +# untar v0.1.0 # -# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. # # The component may contain files which fall under a different license. The # authors of this component should specify the license in the header of such @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "untar v0.1" + echo "untar v0.1.0" echo "" echo "Unpack a .tar file. When the contents of the .tar file is just a single" echo "directory," @@ -476,10 +476,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component untar" -LABEL org.opencontainers.image.created="2024-09-12T15:43:28Z" +LABEL org.opencontainers.image.created="2024-09-12T15:57:22Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox" -LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295" -LABEL org.opencontainers.image.version="v0.1" +LABEL org.opencontainers.image.revision="3143dd6e4c2c3107f79639fe8602d92f3141ad82" +LABEL org.opencontainers.image.version="v0.1.0" VIASHDOCKER fi @@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "untar v0.1" + echo "untar v0.1.0" exit ;; --input) @@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/untar:v0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/craftbox/untar:v0.1.0' fi # print dockerfile diff --git a/target/nextflow/concat_text/.config.vsh.yaml b/target/nextflow/concat_text/.config.vsh.yaml index 2e917c9..d9abf79 100644 --- a/target/nextflow/concat_text/.config.vsh.yaml +++ b/target/nextflow/concat_text/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "concat_text" -version: "v0.1" +version: "v0.1.0" authors: - name: "Toni Verbeiren" roles: @@ -152,7 +152,7 @@ engines: id: "docker" image: "alpine:latest" target_registry: "images.viash-hub.com" - target_tag: "v0.1" + target_tag: "v0.1.0" namespace_separator: "/" setup: - type: "apk" @@ -170,22 +170,22 @@ build_info: engine: "docker|native" output: "target/nextflow/concat_text" executable: "target/nextflow/concat_text/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295" + viash_version: "0.9.0" + git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82" git_remote: "https://github.com/viash-hub/craftbox" package_config: name: "craftbox" - version: "v0.1" + version: "v0.1.0" description: "A collection of custom-tailored scripts and applied tools.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" keywords: - "scripts" - "custom" diff --git a/target/nextflow/concat_text/main.nf b/target/nextflow/concat_text/main.nf index 1490f1e..cb758a8 100644 --- a/target/nextflow/concat_text/main.nf +++ b/target/nextflow/concat_text/main.nf @@ -1,8 +1,8 @@ -// concat_text v0.1 +// concat_text v0.1.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1732,7 +1732,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1803,7 +1805,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1845,7 +1849,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2803,7 +2809,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "concat_text", - "version" : "v0.1", + "version" : "v0.1.0", "authors" : [ { "name" : "Toni Verbeiren", @@ -3001,7 +3007,7 @@ meta = [ "id" : "docker", "image" : "alpine:latest", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1", + "target_tag" : "v0.1.0", "namespace_separator" : "/", "setup" : [ { @@ -3024,22 +3030,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/concat_text", - "viash_version" : "0.9.0-RC7", - "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295", + "viash_version" : "0.9.0", + "git_commit" : "3143dd6e4c2c3107f79639fe8602d92f3141ad82", "git_remote" : "https://github.com/viash-hub/craftbox" }, "package_config" : { "name" : "craftbox", - "version" : "v0.1", + "version" : "v0.1.0", "description" : "A collection of custom-tailored scripts and applied tools.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1'" + ".engines[.type == 'docker'].target_tag := 'v0.1.0'" ], "keywords" : [ "scripts", @@ -3204,7 +3210,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3335,7 +3345,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3343,8 +3354,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3381,6 +3392,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3392,10 +3404,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3480,7 +3491,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/craftbox/concat_text", - "tag" : "v0.1" + "tag" : "v0.1.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/concat_text/nextflow.config b/target/nextflow/concat_text/nextflow.config index dde014a..31a083a 100644 --- a/target/nextflow/concat_text/nextflow.config +++ b/target/nextflow/concat_text/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'concat_text' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1' + version = 'v0.1.0' description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n' author = 'Toni Verbeiren, Dries Schaumont' } diff --git a/target/nextflow/csv2fasta/.config.vsh.yaml b/target/nextflow/csv2fasta/.config.vsh.yaml index 6b10312..7e295eb 100644 --- a/target/nextflow/csv2fasta/.config.vsh.yaml +++ b/target/nextflow/csv2fasta/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "csv2fasta" -version: "v0.1" +version: "v0.1.0" argument_groups: - name: "Inputs" arguments: @@ -192,7 +192,7 @@ engines: id: "docker" image: "python:slim" target_registry: "images.viash-hub.com" - target_tag: "v0.1" + target_tag: "v0.1.0" namespace_separator: "/" setup: - type: "apt" @@ -221,22 +221,22 @@ build_info: engine: "docker|native" output: "target/nextflow/csv2fasta" executable: "target/nextflow/csv2fasta/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295" + viash_version: "0.9.0" + git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82" git_remote: "https://github.com/viash-hub/craftbox" package_config: name: "craftbox" - version: "v0.1" + version: "v0.1.0" description: "A collection of custom-tailored scripts and applied tools.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" keywords: - "scripts" - "custom" diff --git a/target/nextflow/csv2fasta/main.nf b/target/nextflow/csv2fasta/main.nf index e855ba6..54bf7f2 100644 --- a/target/nextflow/csv2fasta/main.nf +++ b/target/nextflow/csv2fasta/main.nf @@ -1,8 +1,8 @@ -// csv2fasta v0.1 +// csv2fasta v0.1.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1728,7 +1728,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1799,7 +1801,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1841,7 +1845,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2799,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "csv2fasta", - "version" : "v0.1", + "version" : "v0.1.0", "argument_groups" : [ { "name" : "Inputs", @@ -3019,7 +3025,7 @@ meta = [ "id" : "docker", "image" : "python:slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1", + "target_tag" : "v0.1.0", "namespace_separator" : "/", "setup" : [ { @@ -3060,22 +3066,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/csv2fasta", - "viash_version" : "0.9.0-RC7", - "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295", + "viash_version" : "0.9.0", + "git_commit" : "3143dd6e4c2c3107f79639fe8602d92f3141ad82", "git_remote" : "https://github.com/viash-hub/craftbox" }, "package_config" : { "name" : "craftbox", - "version" : "v0.1", + "version" : "v0.1.0", "description" : "A collection of custom-tailored scripts and applied tools.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1'" + ".engines[.type == 'docker'].target_tag := 'v0.1.0'" ], "keywords" : [ "scripts", @@ -3316,7 +3322,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3447,7 +3457,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3455,8 +3466,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3493,6 +3504,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3504,10 +3516,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3592,7 +3603,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/craftbox/csv2fasta", - "tag" : "v0.1" + "tag" : "v0.1.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/csv2fasta/nextflow.config b/target/nextflow/csv2fasta/nextflow.config index a194859..2a9168d 100644 --- a/target/nextflow/csv2fasta/nextflow.config +++ b/target/nextflow/csv2fasta/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'csv2fasta' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1' + version = 'v0.1.0' description = 'Convert two columns from a CSV file to FASTA entries. The CSV file can\ncontain an optional header and each row (other than the header) becomes\na single FASTA record. One of the two columns will be used as the names\nfor the FASTA entries, while the other become the sequences. The sequences\ncolumn must only contain characters that are valid IUPAC notation for \nnucleotides or a group thereof (wildcard characters).\n' } diff --git a/target/nextflow/untar/.config.vsh.yaml b/target/nextflow/untar/.config.vsh.yaml index d213d7e..9c48fed 100644 --- a/target/nextflow/untar/.config.vsh.yaml +++ b/target/nextflow/untar/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "untar" -version: "v0.1" +version: "v0.1.0" argument_groups: - name: "Input arguments" arguments: @@ -129,7 +129,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.1" + target_tag: "v0.1.0" namespace_separator: "/" setup: - type: "apt" @@ -146,22 +146,22 @@ build_info: engine: "docker|native" output: "target/nextflow/untar" executable: "target/nextflow/untar/main.nf" - viash_version: "0.9.0-RC7" - git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295" + viash_version: "0.9.0" + git_commit: "3143dd6e4c2c3107f79639fe8602d92f3141ad82" git_remote: "https://github.com/viash-hub/craftbox" package_config: name: "craftbox" - version: "v0.1" + version: "v0.1.0" description: "A collection of custom-tailored scripts and applied tools.\n" info: null - viash_version: "0.9.0-RC7" + viash_version: "0.9.0" source: "src" target: "target" config_mods: - ".requirements.commands := ['ps']\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" keywords: - "scripts" - "custom" diff --git a/target/nextflow/untar/main.nf b/target/nextflow/untar/main.nf index 176485b..48fe97b 100644 --- a/target/nextflow/untar/main.nf +++ b/target/nextflow/untar/main.nf @@ -1,8 +1,8 @@ -// untar v0.1 +// untar v0.1.0 // -// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a -// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -// Data Intuitive. +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. // // The component may contain files which fall under a different license. The // authors of this component should specify the license in the header of such @@ -1728,7 +1728,9 @@ def publishStates(Map args) { def yamlFilename = yamlTemplate_ .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) // TODO: do the pathnames in state_ match up with the outputFilenames_? @@ -1799,7 +1801,9 @@ def publishStatesByConfig(Map args) { def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' def yamlFilename = yamlTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where @@ -1841,7 +1845,9 @@ def publishStatesByConfig(Map args) { // instantiate the template def filename = filenameTemplate .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) if (par.multiple) { // if the parameter is multiple: true, the filename // should contain a wildcard '*' that is replaced with @@ -2799,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "untar", - "version" : "v0.1", + "version" : "v0.1.0", "argument_groups" : [ { "name" : "Input arguments", @@ -2959,7 +2965,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1", + "target_tag" : "v0.1.0", "namespace_separator" : "/", "setup" : [ { @@ -2981,22 +2987,22 @@ meta = [ "runner" : "nextflow", "engine" : "docker|native", "output" : "target/nextflow/untar", - "viash_version" : "0.9.0-RC7", - "git_commit" : "5705b88fa20f267475b5d0ae1ca25dbf55ff1295", + "viash_version" : "0.9.0", + "git_commit" : "3143dd6e4c2c3107f79639fe8602d92f3141ad82", "git_remote" : "https://github.com/viash-hub/craftbox" }, "package_config" : { "name" : "craftbox", - "version" : "v0.1", + "version" : "v0.1.0", "description" : "A collection of custom-tailored scripts and applied tools.\n", - "viash_version" : "0.9.0-RC7", + "viash_version" : "0.9.0", "source" : "src", "target" : "target", "config_mods" : [ ".requirements.commands := ['ps']\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1'" + ".engines[.type == 'docker'].target_tag := 'v0.1.0'" ], "keywords" : [ "scripts", @@ -3167,7 +3173,11 @@ def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { val = val.join(par.multiple_sep) } if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) } [parName, val] } @@ -3298,7 +3308,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def createParentStr = meta.config.allArguments .findAll { it.type == "file" && it.direction == "output" && it.create_parent } .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" } .join("\n") @@ -3306,8 +3317,8 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def inputFileExports = meta.config.allArguments .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } .collect { par -> - def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" } // NOTE: if using docker, use /tmp instead of tmpDir! @@ -3344,6 +3355,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { def procStr = """nextflow.enable.dsl=2 | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } |process $procKey {$drctvStrs |input: | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") @@ -3355,10 +3367,9 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { |$stub |\"\"\" |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } |def parInject = args | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} | .join("\\n") |\"\"\" |# meta exports @@ -3443,7 +3454,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/craftbox/untar", - "tag" : "v0.1" + "tag" : "v0.1.0" }, "tag" : "$id" }'''), diff --git a/target/nextflow/untar/nextflow.config b/target/nextflow/untar/nextflow.config index c736c58..b023cf6 100644 --- a/target/nextflow/untar/nextflow.config +++ b/target/nextflow/untar/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'untar' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1' + version = 'v0.1.0' description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n' }